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Calcium in PDB 4mkf: Crystal Structure of A Stable Adenylate Kinase Variant AKV3

Enzymatic activity of Crystal Structure of A Stable Adenylate Kinase Variant AKV3

All present enzymatic activity of Crystal Structure of A Stable Adenylate Kinase Variant AKV3:
2.7.4.3;

Protein crystallography data

The structure of Crystal Structure of A Stable Adenylate Kinase Variant AKV3, PDB code: 4mkf was solved by S.Moon, D.Jung, E.Bae, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.99 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 34.447, 75.008, 77.195, 90.00, 100.89, 90.00
R / Rfree (%) 15.7 / 20.3

Other elements in 4mkf:

The structure of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3 (pdb code 4mkf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3, PDB code: 4mkf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 4mkf

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Calcium binding site 1 out of 7 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:34.1
occ:1.00
 OE1 A:GLN199 2.3 20.1 1.0
O A:HOH459 2.5 25.2 1.0
O A:HOH585 2.6 30.9 1.0
CD A:GLN199 3.5 19.2 1.0
NE2 A:GLN199 4.3 15.9 1.0
O A:HOH499 4.4 37.8 1.0
CG A:GLN199 4.5 18.6 1.0
OD2 A:ASP207 4.6 16.0 1.0
OD1 A:ASP207 4.8 18.0 1.0
CB A:ASP203 4.8 18.4 1.0

Calcium binding site 2 out of 7 in 4mkf

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Calcium binding site 2 out of 7 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:28.1
occ:1.00
 O A:HOH628 2.2 25.7 1.0
O A:HOH629 2.2 30.7 1.0
OD1 A:ASP203 2.3 23.6 1.0
OD2 A:ASP203 2.8 23.4 1.0
CG A:ASP203 2.9 22.9 1.0
CB A:ASP203 4.4 18.4 1.0
OD2 A:ASP200 4.9 31.3 1.0

Calcium binding site 3 out of 7 in 4mkf

Go back to Calcium Binding Sites List in 4mkf
Calcium binding site 3 out of 7 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca306

b:25.0
occ:1.00
 O A:HOH624 2.3 15.2 1.0
O A:HOH517 2.3 19.9 1.0
O A:GLY73 2.3 19.1 1.0
O A:HOH519 2.6 29.3 1.0
O A:HOH591 2.7 35.2 1.0
C A:GLY73 3.5 18.7 1.0
O A:HOH473 4.2 37.4 1.0
CA A:GLY73 4.2 18.1 1.0
N A:LYS74 4.4 17.7 1.0
O A:HOH538 4.5 22.2 1.0
O A:HOH604 4.5 34.7 1.0
CA A:LYS74 4.5 17.7 1.0
C A:LYS74 5.0 16.0 1.0

Calcium binding site 4 out of 7 in 4mkf

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Calcium binding site 4 out of 7 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:13.3
occ:1.00
 O B:HOH627 2.4 13.8 1.0
O B:HOH631 2.4 12.8 1.0
O B:HOH628 2.4 12.9 1.0
OD2 B:ASP200 2.4 14.8 1.0
O B:HOH629 2.5 14.5 1.0
O B:HOH630 2.5 14.7 1.0
CG B:ASP200 3.4 14.7 1.0
CB B:ASP200 3.7 13.2 1.0
O B:HOH588 4.2 27.1 1.0
OD2 B:ASP203 4.3 13.9 1.0
OD1 B:ASP200 4.5 14.6 1.0
OE1 B:GLU202 4.5 17.9 1.0
CA B:CA305 4.6 21.4 1.0
OD1 B:ASP203 4.8 13.9 1.0
CG B:ASP203 4.8 13.2 1.0

Calcium binding site 5 out of 7 in 4mkf

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Calcium binding site 5 out of 7 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:21.4
occ:1.00
 O B:HOH473 2.3 29.6 1.0
O B:HOH636 2.4 36.5 1.0
OD1 B:ASP200 2.4 14.6 1.0
O B:HOH588 2.5 27.1 1.0
O B:HOH592 2.5 27.5 1.0
OD2 B:ASP200 2.6 14.8 1.0
O B:HOH402 2.6 24.7 1.0
CG B:ASP200 2.9 14.7 1.0
O B:HOH554 4.3 25.7 1.0
CB B:ASP200 4.4 13.2 1.0
O B:HOH630 4.5 14.7 1.0
CA B:CA304 4.6 13.3 1.0
O B:HOH581 4.7 14.9 1.0
O B:HOH631 4.7 12.8 1.0
O B:HOH628 4.9 12.9 1.0

Calcium binding site 6 out of 7 in 4mkf

Go back to Calcium Binding Sites List in 4mkf
Calcium binding site 6 out of 7 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca306

b:14.1
occ:1.00
 OE1 B:GLN199 2.2 12.4 1.0
O B:HOH587 2.3 17.9 1.0
O B:HOH613 2.4 12.8 1.0
O B:HOH614 2.5 16.3 1.0
CD B:GLN199 3.4 11.5 1.0
NE2 B:GLN199 4.0 11.1 1.0
O B:HOH549 4.3 31.9 1.0
OD1 B:ASP207 4.3 13.5 1.0
CB B:ASP203 4.5 12.4 1.0
CG B:GLN199 4.5 11.7 1.0
OD2 B:ASP207 4.5 13.7 1.0
O B:ASP203 4.6 11.5 1.0
CG B:ASP207 4.9 13.0 1.0

Calcium binding site 7 out of 7 in 4mkf

Go back to Calcium Binding Sites List in 4mkf
Calcium binding site 7 out of 7 in the Crystal Structure of A Stable Adenylate Kinase Variant AKV3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of A Stable Adenylate Kinase Variant AKV3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca307

b:13.3
occ:1.00
 O B:HOH625 2.3 13.0 1.0
O A:HOH617 2.4 16.9 1.0
O B:HOH626 2.4 13.6 1.0
O B:LYS40 2.4 13.1 1.0
O B:HOH495 2.4 20.2 1.0
O A:HOH436 2.5 17.3 1.0
O B:HOH586 2.6 19.0 1.0
C B:LYS40 3.5 14.6 1.0
CA B:LYS40 4.0 14.2 1.0
OE2 B:GLU42 4.0 18.3 1.0
CG B:LYS40 4.3 20.0 1.0
O A:LEU215 4.3 20.8 1.0
N A:MET1 4.3 13.6 1.0
CG B:GLU42 4.4 15.3 1.0
OD2 A:ASP108 4.4 12.6 1.0
O A:HOH502 4.4 36.0 1.0
OD1 A:ASP108 4.5 13.5 1.0
O B:MET39 4.6 12.2 1.0
N B:GLU41 4.7 14.2 1.0
CD B:GLU42 4.7 16.9 1.0
CB B:LYS40 4.8 17.0 1.0
O B:HOH560 4.8 35.6 1.0
CG A:ASP108 4.9 12.0 1.0
O B:HOH536 4.9 37.6 1.0

Reference:

S.Moon, D.Jung, G.N.Phillips, E.Bae. An Integrated Approach For Thermal Stabilization of A Mesophilic Adenylate Kinase Proteins 2014.
ISSN: ESSN 1097-0134
PubMed: 24615904
DOI: 10.1002/PROT.24549
Page generated: Wed Jul 9 00:25:28 2025

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